Newfound Bacteria Expand Tree of Life

An anonymous reader writes: It used to be that to find new forms of life, all you had to do was take a walk in the woods. Now it's not so simple. The most conspicuous organisms have long since been cataloged and fixed on the tree of life, and the ones that remain undiscovered don't give themselves up easily. You could spend all day by the same watering hole with the best scientific instruments and come up with nothing. Maybe it's not surprising, then, that when discoveries do occur, they sometimes come in torrents. Find a different way of looking, and novel forms of life appear everywhere. A team of microbiologists based at the University of California, Berkeley, recently figured out one such new way of detecting life. At a stroke, their work expanded the number of known types — or phyla — of bacteria by nearly 50 percent, a dramatic change that indicates just how many forms of life on earth have escaped our notice so far.

Comments

Contentious

[jandersen]

Having only just skimmed the article, I may have missed some imprtant points, but it seems they are basing this discovery on DNA analysis, which all well and good as far as it goes. What is no doubt valid is that this method yields a classification, but what is less certain - or perhaps highly uncertain - is whether this classification reflects the evolutionary phylogeny of the organisms in the study.

The big problem here is that DNA similarities probably only really match descendancy (or evolutionary relationship) well, when we talk about eukaryotes; this is because eukaryotes have sex: they go through cycles of meiosis/mitosis and all that, in which they recombine their genes in very rigorous way which ensures that DNA is inherited from predecessors. Prokaryotes don't have sex - instead they have different forms of lateral gene transfer, in which genes are acquired from many, seemingly unrelated organisms. The result of this is that the gene pool WITHIN what we perceive as 'a single species' of bacteria, like Eschericia coli, can be wildly different. Presumably there are genes within a single strain, that are fairly constant, and might be used to trace progeny, but I don't think anybody knows which they are yet.

Re:Contentious

[Anonymous Coward]

Molecular ecologist/Microbiologist here

Actually, evolutionary relationships by DNA similarity as you said work extremely well within all 3 domains of life. Typically we use a highly conserved gene to establish phylogeny- the most common being the small subunit ribosomal RNA gene (16S for Bacteria/Archaea, and 18S for Eukaryotes). This gene is conserved across all domains of life, and essential for the functioning of the ribosome (The little machine that makes proteins). Without it, the ribosome wouldn't form, and you wouldn't be living. Now, to the point of lateral transfer of genes- much of the genetic lineage of a bacterium is from vertical inheritance after replication of a cell- the cell divides, and is most closely related to the parent cell from which it originated. You get genetic drift as errors crop up in the genomes of bacteria, and these errors are propagated from cell to dividing cell. Eventually these errors either become a new functional gene, a silent mutation, or are enough to kill the cell. Alternatively (As you stated) you get new function via horizontal gene transfer. But essential genes (such as the gene that codes for 16S rRNA) are not transferred horizontally, and can be used to establish a meaningful phylogeny of life.

Now the definition of a species within microbial life is somewhat contentious, and is typically established at a cutoff of 97 percent sequence similarity of the 16S/18S rRNA gene that correlates with a number of chemotaxonomic (functional/structural) changes. Otherwise yes, what differentiates an E. coli from E. albertii can be somewhat arbitrary. But using 16S/18S we can make much more meaningful and broad statements about higher taxonomic levels (Genus, Order, etc.). Binning genomes as Dr. Banfield did, and finding conserved marker genes like 16S in these novel genomes to establish phylogeny also allows us to infer functional traits and give at least some insight into what these uncultured microbes are doing.

Craig Venter first did this in 2004

[peter303]

He combined his love of sailing with ocean microbe sampling to investigate the diversity of life. https://en.wikipedia.org/wiki/...
Incidentally Craig perfected the shotgun decodign technique which accelerated decoding the first human genome in the late 1990s (his of course :-). Now gene sampling is fairly routine way of mapping biomes all over the ecosphere.